CDS&E Initiative @ Rurgers University

Distinguished Seminar Series on Computational and Data-Enabled Science and Engineering (CDS&E)


Computational and Data-Enabled Science and Engineering (CDS&E) is an intellectual discipline that brings together core areas of science and engineering, computer science, and computational and applied mathematics in a concerted effort to use cyberinfrastructure (CI) for scientific discovery and engineering innovations. It is clear that CDS&E has become a central theme in the national research and education agenda, and it is critically important that Rutgers University respond by establishing a core competency in this emerging discipline.

The goal of this distinguished seminar series is to bring national CDS&E leaders to Rutgers to talk about their vision and research. The currently scheduled speakers are listed below. The talks will be held at the Fiber Optics Auditorium, 607 Taylor Road on Busch Campus, and will begin at 10:00 AM. There will be an informal reception before the talks at 9:30AM. Additional details about the talks will be posted at http://nsfcac.rutgers.edu/cdse/seminars/.

Announcement: Seminars of March 08 and March 28 will be held in CAIT Auditorium on Busch Campus and will start at 10:30.

Schedule of Seminars

October 10, 2011: Sangtae Kim, Executive Director of the Morgridge Institute for Research, University of Wisconsin-Madison

October 26, 2011: Edward Seidel, Assistant Director for Mathematical and Physical Sciences, US National Science Foundation

November 28, 2011: David Case, Professor of Chemistry & Chemical Biology, Rutgers University

February 08, 2012: Alan Blatecky, Assistant Director for Office of Cyberinfrastructure, US National Science Foundation

February 20, 2012: Craig Stewart, Executive Director, Pervasive Technology Institute, Associate Dean, Research Technologies, Associate Director, CREST, Indiana University

February 21, 2012: Bob Grossman, Director of Informatics at the Institute for Genomics and Systems Biology, University

March 08, 2012: Chris Johnson, Director, Scientific Computing and Imaging (SCI) Institute, University of Utah

March 28, 2012: Dan Reed, Corporate Vice President, Technology Policy Group Microsoft Corporation


October 10, 2011:

Sangtae Kim, Executive Director of the Morgridge Institute for Research, University of Wisconsin-Madison

Title: Pharmaceutical Informatics and Computer-Aided Drug Discovery

Abstract: The scientific community has witnessed the divergence of the field of "computational biology" into two disjoint communities: one group focused on the "wriggling of molecules" (e.g., molecular dynamics) as governed by the equations of biochemical physics and another revolving around pattern matching and informatics (e.g., sequence alignment). As we enter the petascale era of data-intensive computational science, exciting advances in computer-aided drug discovery can be envisioned in a new niche in the computational biology ecosystem - a niche formed by the reunion of the separated branches of computational biology. In this presentation, we consider some examples from pharmaceutical informatics of data-intensive approaches applied to "objects" that are not simply numbers or static molecular structures but instead are (compute-intensive) dynamic simulations. The relevance of this approach to the rational design of new anti-cancer drugs will also be described.

Short Biography: Sangtae "Sang" Kim was appointed executive director of the new, private not-for-profit Morgridge Institute for Research in September 2008. In this position, he is building a world-class interdisciplinary biomedical research organization from the ground up. Located on the University of Wisconsin-Madison campus, it is intended to become the Midwest's premier, private medical research institute.
Prior to his appointment at the Morgridge Institute, he was the Donald W. Feddersen Distinguished Professor of Mechanical Engineering and Distinguished Professor of Chemical Engineering at Purdue University. His past work experience includes serving the National Science Foundation as director of the division of shared cyberinfrastructure, as well as six years of executive industry experience gained at Lilly Research Laboratories, Pfizer Global Research and Development and Parke-Davis Pharmaceutical Research.
Kim joined the UW-Madison faculty in 1983 and served as chair of the Department of Chemical Engineering from 1995-1997. During his tenure at UW-Madison, he also was granted a courtesy appointment in the Department of Computer Sciences, and was recognized as an exceptional teacher, scholar and intellectual leader.
He earned a Ph.D. in chemical and biological engineering from Princeton University in 1983, following concurrent bachelor's and master's of science degrees from the California Institute of Technology in 1979. In 2001, he was elected a member of the prestigious National Academy of Engineering for his contributions to microhydrodynamics, protein dynamics, and drug discovery through the application of high-performance computing.
Kim currently serves on the science board of the Food and Drug Administration and on the scientific advisory board of Venture Investors of Wisconsin. He has provided advice and technical support to a number of start-up companies, including Alien Technology, a California maker of radio frequency identification (RFID) tags for inventory tracking, and Indigo Biosystems, a software and information management company spun off from Eli Lilly & Co. in 2004.
He has earned numerous professional awards and honors, published and lectured widely as a researcher, contributed to variety of boards and committees and is proud of his many successful graduate students.
Born in Korea, Kim was raised in Canada. He enjoys spending time with his wife and two daughters, both currently in medical school. When not exploring and pushing the boundaries of the intersections of science and technology, he is an amateur historian who especially enjoys reading about the history of science.

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October 26, 2011:

Edward Seidel, Assistant Director for Mathematical and Physical Sciences, US National Science Foundation

Title: The Data and Compute-Driven Transformation of Modern Science

Abstract: We all know that modern science is undergoing a profound transformation as it aims to tackle the complex problems of the 21st Century. It is becoming highly collaborative; problems as diverse as climate change, renewable energy, or the origin of gamma-ray bursts require understanding processes that no single group or community alone has the skills to address. At the same time, after centuries of little change, compute, data, and network environments have grown by 9-12 orders of magnitude in the last few decades. Moreover, science is not only compute-intensive but is dominated now by data-intensive methods. This dramatic change in the culture and methodology of science will require a much more integrated and comprehensive approach to development and deployment of hardware, software, and algorithmic tools and environments supporting research, education, and increasingly collaboration across disciplines.

Short Biography:Edward Seidel is a physicist recognized for his work on numerical relativity and black holes, as well as in high-performance and grid computing. He earned his Ph.D. from Yale University in relativistic astrophysics. He was a professor at the Max Planck Institute for Gravitational Physics (Albert-Einstein-Institute, or AEI) in Germany from 1996-2003. There, Seidel founded and led AEI's numerical relativity and e-science groups, which became leaders in solving Einstein's equations using large-scale computers, and in distributed and grid computing. He also was a senior research scientist at the National Center for Supercomputing Applications and associate professor in the Physics Department at the University of Illinois, Urbana-Champaign.
In 2003, Louisiana State University recruited Seidel to lead its investment in the Governor's Information Technology Initiative, and he became founding director of LSU's Center for Computation & Technology. Seidel served as CCT director from 2003-2008. Seidel also is the Floating Point Systems Professor in LSU's Departments of Physics & Astronomy and Computer Science. In addition to leading the CCT, he helped initiate, and was the chief scientist for, the $40M Louisiana Optical Network Initiative. He is a recipient of the IEEE Sidney Fernbach Award, the Gordon Bell Prize, and Heinz-Billing Prize, and is a fellow of the American Physical Society.
In June 2008, the National Science Foundation selected Seidel as its director for the Office of Cyberinfrastructure (OCI). He began this position Sept. 1, 2008, in which he oversees advances in supercomputing, high-speed networking, data storage and software development on a national level. He has recently assumed the role of Assistant Director for Mathematics and Physical Sciences at NSF.

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November 28, 2011:

David Case, Professor of Chemistry & Chemical Biology, Rutgers University

Title: Molecular dynamics simulations of proteins and nucleic acids

Abstract: Molecular dynamics simulations of biomolecules have become an increasingly important tool in the fields of biochemistry and molecular biology. They also provide an interesting set of challenges for distributed and high-performance computing platforms. I will give an overview of ways in which such simulations are used in a biological realm, but devote most of the talk to a discussion of the computations themselves, examining challenges and opportunities in three main areas: tightly-coupled and highly parallel machines, more loosely coupled and very distributed networks, and the use of graphical processing units (GPUs) as an affordable alternative architecture.

Short Biography: David Case received a Bachelor's degree in Chemistry from Michigan State, and a Ph.D. in chemical physics from Harvard. He joined the Department of Chemistry and Chemical Biology and the BioMaPS Insitute at Rutgers in 2008, following work at U.C. Davis and The Scripps Research Institute. His research focusses on theoretical chemistry of biomolecules. Particular areas of interest include molecular dynamics simulations of proteins and nucleic acids; electronic structure calculations of transition-metal complexes that model active sites in metalloenzymes; development and application of methods for NMR structure determination; ligand-protein and ligand-nucleic acid docking and computational drug design. He is a Fellow of the Royal Society of Chemistry.
Prof. Case oversees development of the Amber suite of programs for biomolecular simulation. A large group of volunteers from many places contributes to computer codes that are used in over 900 labs to carry out molecular dynamics analysis of proteins, carbohydrates and nucleic acids. Simulations using Amber can be used to study many aspects of the structure and dynamics of biomolecules. Typical current research projects in the Case group include: the energetics of binding of drug candidates to enzymes; mechanical properties of nucleic acids; conformational preferences of polysaccharides; and the determination of solution structures by nuclear magnetic resonance (NMR). The group is also active in the development of new energy functions (force fields) and simulation methods to help make these calculations more predictive.

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February 08, 2012:

Alan Blatecky, Assistant Director for Office of Cyberinfrastructure, US National Science Foundation

Title: Cyberinfrastructure : a catalyst which is transforming science

Abstract: Innovative information technologies are transforming the fabric of society and data is the new currency for science, education, government and commerce. Decades of investments in observing platforms, computational infrastructure, and model development have already led to important breakthroughs in the sciences and engineering. The need to interrogate and manage the ever-increasing, unprecedented volumes of data and simulations being generated from these components of research-enabling infrastructure are transforming the very conduct of the science and engineering. Commoditization of both hardware and software is creating an era of significant disruptions. One disruption is the changing nature and role of next generation computing and technologies. A second disruption is that the ubiquitous availability of a wide range of technologies will fundamentally change the types of algorithms and software that must be implemented for research and education. A third disruption is the emerging transformation of the institutions engaged in the higher education enterprise as there will be much less connection between researchers and the physical place of their institutions. These factors are leading to new models for compute and data-intensive science that will be organized dynamically around research questions, domains, expertise, and resources, and will present new challenges to geographically-centered research efforts, including traditional departments and campuses.

Short Biography: Alan Blatecky has been appointed as director for the Office of Cyberinfrastructure (OCI) at the National Science Foundation (NSF). Blatecky has been the acting office head for OCI since June 2010.
Prior to joining NSF, Blatecky was deputy director of the Renaissance Computing Institute (RENCI) and still serves as chief scientist for cyberinfrastructure there. Previous positions include executive director of research and programs at the San Diego Supercomputing Center; acting division director for Advanced Networking Infrastructure and Research in the Computer Information Science and Engineering Directorate at NSF; vice president of information technology at MCNC (Microelectronics Center of North Carolina); vice president of networking at the North Carolina Supercomputing Center; and played a central role in establishing the North Carolina Research and Education Network.
Blatecky has focused on establishing, developing and operating a variety of advanced high-performance networking, computing, data, and visualization facilities, as well as developing new research programs and initiatives including several business start-ups. He has also been deeply involved in the research, development and deployment of cyberinfrastructure and collaborative technologies to support multidisciplinary research and education, and has served on many state, national and international networking and computing boards and commissions.
Blatecky has four master's degrees including an MBA from the Fuqua School of Business (Duke University), a Master of Arts from Duke University and two master's degrees in Theology from Princeton Theological Seminary, Princeton, N.J.

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February 20, 2012:

Craig Stewart, Executive Director, Pervasive Technology Institute, Associate Dean, Research Technologies, Associate Director, CREST, Indiana University

Title: Cyberinfrastructure begins at home

Abstract: Proclamations about the future of cyberinfrastructure in academia abound. Many such current proclamations can be summarized as "just do it all in the cloud." Clouds may be a good solution for many computing problems, but computational clouds are not magic fairy dust .... You can't just sprinkle the words "cloud computing" on any given problem and thereby solve it. IU's experience with cyberinfrastructure in academia demonstrates that the best order of operations is to set university goals and strategy first, and design cyberinfrastructure facilities and computational science research in ways that support the core university goals. IU's history in computing supporting academic research goes back to the 1950s. Oiver the past decade and a half IU has developed an excellent local cyberinfrastructure and a IT R&D organization - the Pervasive Technology Institute - which is well regarded locally and very successful at the in securing federal and non-federal grants and contracts. This talk will describe how IU has implemented it's IT strategy based on university goals, and discuss some of the common challenges facing academia as regards CI facilities and the need for more compositional and data intensive research and development centers. And IU does use clouds ... this talk will describe the circumstances in which cloud facilities seem to be the best solution to real problems.

Short Biography: Craig Stewart is the Executive Director of the Pervasive Technology Institute (PTI), IU's flagship initiative for advanced information technology research, development, and delivery in support of research, scholarship, and artistic performances. Stewart is Associate Dean for Research Technologies, and leads the Research Technologies Division of University Information Technology Services.
The mission of the Pervasive Technology Institute is to improve quality of life in Indiana and the world by inventing, developing, deploying and delivering innovations in information technology. Stewart is particularly involved in leading cyberinfrastructure services affiliated with PTI, and PTI's activities in economic development, training, education, and outreach. Stewart also leads the activities of PTI Service and Cyberinfrastructure Centers - the UITS Research Technologies Division and the National Center for Genome Analysis Support (NCGAS).
The Research Technologies (RT) division of University Information Technology Services (UITS), which serves the research and scholarship missions of Indiana University. Research Technologies seeks to enhance the quality and quantity of IU research by providing the best possible computation, storage, and visualization facilities and support for IU researchers. The Research Technologies division pioneers the frontiers of advanced computing as a research and development endeavor, and supports research and development through purposeful university/government/industry partnerships and extramural grants. The RT Division also supported collaboration between and among PTI, the School of Informatics and Computing, College of Arts and Sciences, School of Fine Arts, IU School of Medicine, and other academic units at Indiana University.
The National Center for Genome Analysis Support is funded by the NSF to deliver hardened versions of important open source genome analysis applications to the US scientific community, and support use of these applications on a variety of systems, including XSEDE, the IU Mason system, and the "cluster on demand" commercially delivered Rockhopper cluster owned and managed by Penguin Computing Inc. NCGAS will focus particularly on one of the most challenging problems in genome science today - assembly of genomes from next generation sequencers.
Stewart has been very active in the high performance computing for many years, including being very active in the early days of HPC applications in biology. Stewart is a past chair of the Coalition for Academic Scientific Computation (2008-2009), during which time he testified about the importance of high performance computing before the House Science and Technology Committee. Most recently Stewart served as a member of the National Science Foundation Advisory Committee on CyberInfrastructure, and Chair of the ACCI Task Force on Campus Bridging (2010-2011).
Stewart has had a long career in IT at Indiana University, with extensive experience in leading and managing services to support researchers at IU, including past appointments as Director of the Center for Statistical and Mathematical Computing, Research and Academic Computing, Indiana Genomics Initiative Information Technology Core; and Special Assistant for the Life Sciences, IU Office of the Vice President for Research. Stewart is an Adjunct Professor in the School of Informatics, and also holds adjunct appointments in the Department of Medical Genetics (IU School of Medicine) and Biology (IU Bloomington). Stewart has served as a Visiting Faculty Member in Computer Science, University of Stuttgart, and as a Fulbright Senior Scholar at the Technische Universitaet Dresden (Germany). He has a Ph.D. in Ecology and Evolutionary Biology from Indiana University and a Bachelor of Arts degree in Mathematics and Biology from Wittenberg University. Most of his publications are online in the IU Scholarworks Digital Repository (scholarworks.iu.edu).

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February 21, 2012:

Bob Grossman, Director of Informatics at the Institute for Genomics and Systems Biology, University of Chicago and the Open Cloud Consortium

Title: Science Clouds and Their Impact on Big Data Science

Abstract: Just as cloud computing as transformed commercial IT, science clouds are beginning to impact science, especially data intensive science. In this talk, we give an introduction to cloud computing and to science clouds.
We also describe the Open Science Data Cloud (OSDC), a science cloud that is operated by the not-for-profit Open Cloud Consortium. The OSDC is a persistent cloud-based infrastructure that allows scientists to manage, analyze, integrate and share medium to large size scientific datasets. The OSDC contains data from a variety of scientific disciplines, from earth science to biology. The OSDC is currently one of the largest cloud-based infrastructures devoted to scientific data in the world.

Short Biography: Robert Grossman is a faculty member at the University of Chicago. He is the Director of Informatics at the Institute for Genomics and Systems Biology, a Senior Fellow at the Computation Institute, and a Professor of Medicine. His research group focuses on bioinformatics, cloud computing, data intensive computing, predictive modeling, and related areas. He is also a Partner at Open Data Group, which builds predictive models over big data, and the Chair of the Open Cloud Consortium. More information about him can be found at rgrossman.com

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March 08, 2012:

Chris Johnson, Director, Scientific Computing and Imaging (SCI) Institute, University of Utah

Title: Visual Computing: Making Sense of a Complex World

Abstract: Computers are now extensively used throughout science, engineering, and medicine. Advances in computational geometric modeling, imaging, and simulation allow researchers to build and test models of increasingly complex phenomena and thus to generate unprecedented amounts of data. These advances have created the need to make corresponding progress in our ability to understand large amounts of data and information arising from multiple sources. In fact, to effectively understand and make use of the vast amounts of information being produced is one of the greatest scientific challenges of the 21st Century. Visual computing, which relies on and takes advantage of, the interplay among techniques of visualization, large-scale computing, data management, and imaging, is fundamental to understanding models of complex phenomena, which are often multi-disciplinary in nature. In this talk, I will provide examples of interdisciplinary visual computing and imaging research at the Scientific Computing and Imaging (SCI) Institute as applied to important problems in science, engineering, and medicine.

Short Biography: Chris Johnson directs the Scientific Computing and Imaging (SCI) Institute at the University of Utah where he is a Distinguished Professor of Computer Science and holds faculty appointments in the Departments of Physics and Bioengineering. His research interests are in the areas of scientific computing and scientific visualization. Dr. Johnson founded the SCI research group in 1992, which has since grown to become the SCI Institute employing over 200 faculty, staff and students. Professor Johnson serves on several international journal editorial boards, as well as on advisory boards to several national research centers. Professor Johnson has received several awards, including the the NSF Presidential Faculty Fellow (PFF) award from President Clinton in 1995 and the Governor's Medal for Science and Technology from Governor Michael Leavitt in 1999. He is a Fellow of the American Institute for Medical and Biological Engineering, a Fellow of the American Association for the Advancement of Science, and in 2009 he was elected a Fellow of the Society for Industrial and Applied Mathematics (SIAM) and received the Utah Cyber Pioneer Award. In 2010 Professor Johnson received the Rosenblatt Award from the University of Utah and the IEEE Visualization Career Award.

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March 28, 2012:

Dan Reed, Corporate Vice President, Technology Policy Group Microsoft Corporation

Title: Technical Computing: Past, Present, Future

Abstract: Computational science and engineering are moving rapidly from a world of purely homogeneous and local resources to a much more complex world of distributed software and systems, virtual organizations and cloud services. In science, a tsunami of new experimental and computational data and a suite of increasingly ubiquitous sensors pose vexing problems in data analysis, transport, visualization and collaboration. In engineering, modeling tools and multidisciplinary manufacturing pose new challenges. In both cases, many of the most interesting problems increasingly lie at the intersection of individual disciplines, requiring teams from diverse backgrounds to work together across intellectual and cultural barriers.
Let's step back and think about the longer term future. Where is the technology going and what are the implications? What are the lessons that can be gleaned from the history of high-performance computing, technically, organizationally and politically? What are the educational and workforce implications? This talk will examine the scientific, technical and social issues around high-performance computing, computational science, research empowerment and new scientific domains.

Short Biography: As corporate vice president of the Technology Policy Group, Dr. Dan Reed helps shape Microsoft's long-term vision for technology innovations and the company's associated policy engagement with governments and institutions around the world. Given the centrality of information technology to communication and social interaction, research and development, education and learning, health and safety, the environment, and economic development, such strategic technology identification and policy coordination are critical to the company's future. In this capacity, Reed reports to and works closely with Craig Mundie, Microsoft's chief research and strategy officer.
The Technology Policy Group regularly publishes technical perspectives and engages in strategic technical projects on security and privacy, telecommunications and spectrum allocation, energy and environment, science and technology, STEM education and workforce, and the unlimited potential for cloud computing, among other topics, to illustrate alternative future possibilities and outcomes. Reed and his team frequently meet with various members of local and national governments, as well as nongovernmental organizations and industry thought leaders both in the U.S. and globally, to discuss technology advancements on the horizon and the many ways they will reshape our world.
Reed joined Microsoft in December 2007 as scalable and multicore computing strategist. In February 2008, he took on the added responsibility of directing a new Cloud Computing Futures initiative, which explored new approaches to cloud services and datacenter design, including ways to reduce hardware costs and power consumption, and increasing datacenters' adaptability and resilience to failure. In June 2009, Reed led the formation of the eXtreme Computing Group (XCG) within Microsoft Research, with the goal of developing new technologies and constructing integrated, solution-based prototypes. Soon thereafter, Reed added the role of corporate vice president, Technology Policy, and as a result of the growing opportunities and responsibilities within this area, began to focus solely on technology policy in July 2011.
Before coming to Microsoft, Reed held a number of strategic positions, including Gutgsell Professor, head of the Department of Computer Science and director of the National Center for Supercomputing Applications at the University of Illinois, Chancellor's Eminent Professor at the University of North Carolina (UNC) at Chapel Hill, and founding director of UNC's Renaissance Computing Institute. He was also the Chancellor's senior advisor for Strategy and Innovation at UNC.
In addition to his technical activities, Reed has been deeply involved in policy initiatives related to science, technology and innovation. He currently serves as a member of the U.S. Federal Communications Commission's Technical Advisory Committee and has served as a member of the U.S. President's Council of Advisors on Science and Technology (PCAST) and chair of the computational science subcommittee of the President's Information Technology Advisory Committee (PITAC).

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